In mid-June 2019, 3 months after cyclone Idai landfall in Mozambique, health authorities of Nhamatanda district reported an outbreak of Pellagra. Applying a mixed-method protocol, we carried out an investigation to characterize cases of pellagra, identify the associated factors for the outbreak using a case-control study, and explore the perceived impact on food security (availability, access, and usage) before and after Idai. We collected data from 121 cases and 121 controls and conducted in-depth interviews with 69 heads of households. The cases were more likely to be female (P < 0.01) and less educated (P < 0.01) than controls. Insufficient consumption of chicken and peanut before cyclone Idai arrival were statistically associated with pellagra (P < 0.05). From interviewed households' heads, 51% were experiencing food shortages even before the cyclone hit. Cyclone Idai served as a trigger to reduce niacin consumption below the threshold that protected Nhamatanda population from pellagra and caused a ≈2,300 case (707.9/100,000 inhabitants) outbreak.